{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T04:50:28Z","timestamp":1791003028658,"version":"4.1.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,16]],"date-time":"2022-10-16T00:00:00Z","timestamp":1665878400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2020M3A9G7103933"],"award-info":[{"award-number":["2020M3A9G7103933"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Institute of Information & communications Technology Planning & Evaluation","award":["2021-0-02068"],"award-info":[{"award-number":["2021-0-02068"]}]},{"DOI":"10.13039\/501100014364","name":"Samsung Science and Technology Foundation","doi-asserted-by":"publisher","award":["SSTF-BA1901-08"],"award-info":[{"award-number":["SSTF-BA1901-08"]}],"id":[{"id":"10.13039\/501100014364","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Atomic-level knowledge of protein-ligand interactions allows a detailed understanding of protein functions and provides critical clues to discovering molecules regulating the functions. While recent innovative deep learning methods for protein structure prediction dramatically increased the structural coverage of the human proteome, molecular interactions remain largely unknown. A new database, HProteome-BSite, provides predictions of binding sites and ligands in the enlarged 3D human proteome. The model structures for human proteins from the AlphaFold Protein Structure Database were processed to structural domains of high confidence to maximize the coverage and reliability of interaction prediction. For ligand binding site prediction, an updated version of a template-based method GalaxySite was used. A high-level performance of the updated GalaxySite was confirmed. HProteome-BSite covers 80.74% of the UniProt entries in the AlphaFold human 3D proteome. Predicted binding sites and binding poses of potential ligands are provided for effective applications to further functional studies and drug discovery. The HProteome-BSite database is available at https:\/\/galaxy.seoklab.org\/hproteome-bsite\/database and is free and open to all users.<\/jats:p>","DOI":"10.1093\/nar\/gkac873","type":"journal-article","created":{"date-parts":[[2022,10,16]],"date-time":"2022-10-16T09:58:04Z","timestamp":1665914284000},"page":"D403-D408","source":"Crossref","is-referenced-by-count":18,"title":["HProteome-BSite: predicted binding sites and ligands in human 3D proteome"],"prefix":"10.1093","volume":"51","author":[{"given":"Jiho","family":"Sim","sequence":"first","affiliation":[{"name":"Department of Chemistry, Seoul National University , Seoul \u00a008826, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sohee","family":"Kwon","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Seoul National University , Seoul \u00a008826, Republic of Korea"},{"name":"Galux Inc , Gwanak-gu , Seoul \u00a008738, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1419-9888","authenticated-orcid":false,"given":"Chaok","family":"Seok","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Seoul National University , Seoul \u00a008826, Republic of Korea"},{"name":"Galux Inc , Gwanak-gu , Seoul \u00a008738, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,10,16]]},"reference":[{"key":"2023010804204208800_B1","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with alphafold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2023010804204208800_B2","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1126\/science.abj8754","article-title":"Accurate prediction of protein structures and interactions using a three-track neural network","volume":"373","author":"Baek","year":"2021","journal-title":"Science"},{"key":"2023010804204208800_B3","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023010804204208800_B4","doi-asserted-by":"crossref","first-page":"D654","DOI":"10.1093\/nar\/gkab920","article-title":"Kincore: a web resource for structural classification of protein kinases and their inhibitors","volume":"50","author":"Modi","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023010804204208800_B5","doi-asserted-by":"crossref","first-page":"D54","DOI":"10.1093\/nar\/gkab1058","article-title":"APPRIS: selecting functionally important isoforms","volume":"50","author":"Rodriguez","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023010804204208800_B6","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.csbj.2020.02.008","article-title":"Exploring the computational methods for protein-ligand binding site prediction","volume":"18","author":"Zhao","year":"2020","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"2023010804204208800_B7","doi-asserted-by":"crossref","first-page":"D437","DOI":"10.1093\/nar\/gkaa1038","article-title":"RCSB protein data bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences","volume":"49","author":"Burley","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023010804204208800_B8","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1093\/bioinformatics\/btu626","article-title":"PDB-wide collection of binding data: current status of the PDBbind database","volume":"31","author":"Liu","year":"2015","journal-title":"Bioinformatics"},{"key":"2023010804204208800_B9","doi-asserted-by":"crossref","first-page":"D1096","DOI":"10.1093\/nar\/gks966","article-title":"BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions","volume":"41","author":"Yang","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023010804204208800_B10","doi-asserted-by":"crossref","first-page":"2423","DOI":"10.1016\/j.jmb.2019.05.024","article-title":"Updates to binding MOAD (Mother of all databases): polypharmacology tools and their utility in drug repurposing","volume":"431","author":"Smith","year":"2019","journal-title":"J. Mol. Biol."},{"key":"2023010804204208800_B11","doi-asserted-by":"crossref","first-page":"D399","DOI":"10.1093\/nar\/gku928","article-title":"sc-PDB: a 3D-database of ligandable binding sites\u201310 years on","volume":"43","author":"Desaphy","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2023010804204208800_B12","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/j.str.2018.02.001","article-title":"An augmented pocketome: detection and analysis of small-molecule binding pockets in proteins of known 3D structure","volume":"26","author":"Bhagavat","year":"2018","journal-title":"Structure"},{"key":"2023010804204208800_B13","doi-asserted-by":"crossref","first-page":"4097","DOI":"10.1021\/acs.jcim.1c00454","article-title":"ProBiS-Dock database: a web server and interactive web repository of small ligand-protein binding sites for drug design","volume":"61","author":"Konc","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"2023010804204208800_B14","doi-asserted-by":"crossref","DOI":"10.1101\/2021.11.26.470110","article-title":"AlphaFill: enriching the alphafold models with ligands and co-factors","author":"Hekkelman","year":"2021"},{"key":"2023010804204208800_B15","doi-asserted-by":"crossref","first-page":"967","DOI":"10.3390\/biom12070967","article-title":"CavitySpace: a database of potential ligand binding sites in the human proteome","volume":"12","author":"Wang","year":"2022","journal-title":"Biomolecules"},{"key":"2023010804204208800_B16","doi-asserted-by":"crossref","first-page":"W593","DOI":"10.1093\/nar\/gkac389","article-title":"PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures","volume":"50","author":"Jakubec","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023010804204208800_B17","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/s41592-022-01490-7","article-title":"ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction","volume":"19","author":"Tubiana","year":"2022","journal-title":"Nat. Methods"},{"key":"2023010804204208800_B18","doi-asserted-by":"crossref","first-page":"W210","DOI":"10.1093\/nar\/gku321","article-title":"GalaxySite: ligand-binding-site prediction by using molecular docking","volume":"42","author":"Heo","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023010804204208800_B19","doi-asserted-by":"crossref","first-page":"2167","DOI":"10.1093\/bib\/bby078","article-title":"Binding site matching in rational drug design: algorithms and applications","volume":"20","author":"Naderi","year":"2019","journal-title":"Brief. Bioinform"},{"key":"2023010804204208800_B20","doi-asserted-by":"crossref","first-page":"2722","DOI":"10.1093\/bioinformatics\/btt473","article-title":"lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests","volume":"29","author":"Mariani","year":"2013","journal-title":"Bioinformatics"},{"key":"2023010804204208800_B21","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1093\/bioinformatics\/bti125","article-title":"Protein homology detection by HMM-HMM comparison","volume":"21","author":"Soding","year":"2005","journal-title":"Bioinformatics"},{"key":"2023010804204208800_B22","doi-asserted-by":"crossref","first-page":"2647","DOI":"10.1002\/jcc.23438","article-title":"GalaxyDock2: protein-ligand docking using beta-complex and global optimization","volume":"34","author":"Shin","year":"2013","journal-title":"J. Comput. Chem."},{"key":"2023010804204208800_B23","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/s13321-018-0285-8","article-title":"P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure","volume":"10","author":"Krivak","year":"2018","journal-title":"J. Cheminform."},{"key":"2023010804204208800_B24","doi-asserted-by":"crossref","first-page":"W471","DOI":"10.1093\/nar\/gks372","article-title":"COFACTOR: an accurate comparative algorithm for structure-based protein function annotation","volume":"40","author":"Roy","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023010804204208800_B25","doi-asserted-by":"crossref","first-page":"2588","DOI":"10.1093\/bioinformatics\/btt447","article-title":"Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment","volume":"29","author":"Yang","year":"2013","journal-title":"Bioinformatics"},{"key":"2023010804204208800_B26","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/nrd.2016.230","article-title":"A comprehensive map of molecular drug targets","volume":"16","author":"Santos","year":"2017","journal-title":"Nat. Rev. Drug Discov."},{"key":"2023010804204208800_B27","doi-asserted-by":"crossref","first-page":"W431","DOI":"10.1093\/nar\/gkab314","article-title":"Mol* viewer: modern web app for 3D visualization and analysis of large biomolecular structures","volume":"49","author":"Sehnal","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023010804204208800_B28","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.ccr.2010.06.018","article-title":"SIK2 is a centrosome kinase required for bipolar mitotic spindle formation that provides a potential target for therapy in ovarian cancer","volume":"18","author":"Australian Ovarian Cancer Study Group","year":"2010","journal-title":"Cancer Cell"},{"key":"2023010804204208800_B29","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/j.ccell.2016.06.020","article-title":"Salt-Inducible kinase 2 couples ovarian cancer cell metabolism with survival at the adipocyte-rich metastatic niche","volume":"30","author":"Miranda","year":"2016","journal-title":"Cancer Cell"},{"key":"2023010804204208800_B30","doi-asserted-by":"crossref","first-page":"2739","DOI":"10.1002\/jcc.26050","article-title":"GalaxyDock3: Protein\u2013ligand docking that considers the full ligand conformational flexibility","volume":"40","author":"Yang","year":"2019","journal-title":"J. Comput. Chem."},{"key":"2023010804204208800_B31","doi-asserted-by":"crossref","first-page":"16986","DOI":"10.1073\/pnas.1215450109","article-title":"Phosphorylation of CRTC3 by the salt-inducible kinases controls the interconversion of classically activated and regulatory macrophages","volume":"109","author":"Clark","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2023010804204208800_B32","doi-asserted-by":"crossref","first-page":"eaav9701","DOI":"10.1126\/scitranslmed.aav9701","article-title":"Targeting diacylglycerol acyltransferase 2 for the treatment of nonalcoholic steatohepatitis","volume":"11","author":"Amin","year":"2019","journal-title":"Sci. Transl. Med."},{"key":"2023010804204208800_B33","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/s41586-021-03828-1","article-title":"Highly accurate protein structure prediction for the human proteome","volume":"596","author":"Tunyasuvunakool","year":"2021","journal-title":"Nature"},{"key":"2023010804204208800_B34","doi-asserted-by":"crossref","first-page":"7173","DOI":"10.1021\/acs.jmedchem.5b01006","article-title":"Discovery and optimization of imidazopyridine-based inhibitors of diacylglycerol acyltransferase 2 (DGAT2)","volume":"58","author":"Futatsugi","year":"2015","journal-title":"J. Med. Chem."},{"key":"2023010804204208800_B35","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/s41586-020-2280-2","article-title":"Structure and mechanism of human diacylglycerol O-acyltransferase 1","volume":"581","author":"Wang","year":"2020","journal-title":"Nature"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D403\/48440674\/gkac873.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D403\/48440674\/gkac873.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T04:21:18Z","timestamp":1673151678000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D403\/6761731"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,16]]},"references-count":35,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2022,10,16]]},"published-print":{"date-parts":[[2023,1,6]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac873","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,6]]},"published":{"date-parts":[[2022,10,16]]}}}